Contacts of the helix formed by residues 11 - 22 (chain A) in PDB entry 3H90
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A SER* 1.3 70.7 - - - +
12A ALA* 1.3 54.7 + - - +
13A ALA* 2.9 8.1 - - - +
14A ILE* 3.1 61.2 + - - +
64A LEU* 4.7 17.6 - - + +
79A GLU* 3.3 25.5 + - - -
142A THR* 3.1 29.1 + - - +
143A GLN* 5.0 3.0 - - - +
144A SER* 3.3 21.2 + - - +
145A GLN 5.3 0.2 - - - +
240A GLY 4.0 2.6 - - - -
241A PRO* 3.3 51.0 - - + +
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 5.6 5.8 - - + -
10A SER* 2.8 15.1 + - - +
11A ARG* 1.3 73.2 - - - +
13A ALA* 1.3 64.0 + - - +
14A ILE 3.2 1.3 - - - -
15A ALA* 3.3 18.6 - - + +
16A ALA* 3.2 20.1 + - - +
64A LEU* 5.7 2.4 - - - +
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Residues in contact with ALA 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A VAL* 5.3 9.8 - - + +
10A SER 2.7 16.1 + - - +
11A ARG 4.5 0.2 - - - -
12A ALA* 1.3 79.6 - - - +
14A ILE* 1.3 59.9 + - - +
16A ALA* 3.3 19.7 + - - +
17A THR 3.5 3.8 + - - -
134A PHE* 5.0 1.4 - - - -
137A TRP* 5.7 7.0 - - + -
138A VAL* 3.3 27.8 - - + +
141A ARG* 5.6 3.8 - - + -
142A THR* 4.3 10.8 - - + -
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Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ARG* 3.1 54.7 - - - +
12A ALA 3.2 0.4 - - - -
13A ALA* 1.3 72.8 - - - +
15A ALA* 1.3 73.2 + - - +
16A ALA 3.0 1.1 - - - -
17A THR* 2.8 27.9 + - - +
18A ALA* 3.3 6.8 + - - +
60A VAL* 3.7 32.2 - - + +
63A SER* 5.4 0.2 - - - +
64A LEU* 4.0 15.3 - - + -
79A GLU* 4.4 8.7 - - - +
138A VAL* 4.3 1.3 - - + -
142A THR* 3.5 22.7 - - + +
144A SER* 4.1 13.0 - - - +
147A VAL* 3.8 11.0 - - + +
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 3.3 23.9 + - + +
14A ILE* 1.3 86.1 - - + +
16A ALA* 1.3 61.2 + - - +
18A ALA* 3.3 12.0 - - - +
19A MET* 3.1 25.5 - - + +
57A LEU* 4.4 1.5 - - + +
60A VAL* 4.5 11.0 - - + -
61A ARG* 5.2 8.1 - - - +
64A LEU* 5.1 8.3 - - + -
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA 3.2 11.4 + - - +
13A ALA* 3.4 13.5 - - - +
14A ILE 3.0 0.8 - - - -
15A ALA* 1.3 76.8 - - - +
17A THR* 1.3 60.9 + - - +
18A ALA 3.4 0.2 + - - -
19A MET* 3.4 15.0 + - - +
20A ALA* 3.2 17.5 + - - +
134A PHE* 4.1 16.1 - - + -
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Residues in contact with THR 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ALA 3.5 3.8 + - - +
14A ILE* 2.8 36.8 - - - +
16A ALA* 1.3 75.4 - - - +
18A ALA* 1.3 53.3 + - - +
20A ALA* 2.9 11.6 + - - +
21A SER* 2.8 32.6 + - - -
131A LEU* 4.9 0.3 - - - +
134A PHE* 3.7 6.5 - - - -
135A GLN* 3.6 24.8 + - - +
138A VAL* 3.8 23.8 - - + -
147A VAL* 3.6 26.8 - - + +
150A ASP* 5.2 2.3 + - - -
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ILE 3.3 6.9 + - - +
15A ALA 3.3 14.5 + - - +
16A ALA 3.2 0.4 - - - -
17A THR* 1.3 79.3 - - - +
19A MET* 1.3 59.7 + - - +
21A SER* 3.3 19.4 - - - -
22A LEU* 3.5 13.7 - - - +
53A SER 4.1 3.9 - - - +
56A ASN* 5.2 4.0 - - - +
57A LEU* 3.5 39.2 - - + +
60A VAL* 4.5 9.2 - - + -
150A ASP* 5.4 2.9 - - - -
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Residues in contact with MET 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ALA* 3.1 32.3 - - + +
16A ALA* 3.6 13.5 - - - +
18A ALA* 1.3 72.0 - - - +
20A ALA* 1.3 58.6 + - - +
21A SER 3.0 2.0 - - - -
22A LEU* 2.6 35.1 + - + +
23A LEU* 2.8 10.6 + - - +
57A LEU* 4.2 16.2 - - + -
61A ARG* 3.4 29.4 - - - +
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Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA 3.2 6.4 + - - +
17A THR* 2.9 11.8 + - - +
19A MET* 1.3 77.4 - - - +
21A SER* 1.3 56.4 + - - +
23A LEU* 2.8 28.8 - - + +
131A LEU* 3.3 21.4 - - + +
134A PHE* 3.5 37.7 - - + -
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A THR 2.8 9.4 + - - -
18A ALA* 3.3 11.9 - - - -
19A MET 3.0 0.2 - - - -
20A ALA* 1.3 74.1 - - - +
22A LEU* 1.3 58.5 + - - +
23A LEU 3.0 5.4 - - - -
24A LEU* 3.1 31.9 + - - +
49A ASP 4.7 0.3 + - - -
53A SER* 2.7 31.6 + - - -
131A LEU* 4.0 11.6 - - - +
135A GLN* 5.0 1.3 - - - -
150A ASP* 3.5 22.2 - - - -
154A TYR* 3.0 8.7 + - - -
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ALA 3.5 14.1 - - - +
19A MET* 2.6 25.5 + - + +
21A SER* 1.3 78.6 - - - +
23A LEU* 1.3 57.6 + - - -
24A LEU* 3.0 2.0 - - - -
25A LEU* 2.9 50.6 - - + +
26A ILE* 5.7 0.2 - - - +
50A ILE* 4.3 6.5 - - - +
53A SER 3.7 14.6 - - - +
54A LEU* 3.7 28.0 - - + +
57A LEU* 3.8 27.8 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il